Examples with XmlParseException cbit.vcell.xml.XmlParseException used on opensource projects

Example 16 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class MathVerifier method testMathGeneration.

public MathGenerationResults testMathGeneration(KeyValue simContextKey) throws SQLException, ObjectNotFoundException, DataAccessException, XmlParseException, MappingException, MathException, MatrixException, ExpressionException, ModelException, PropertyVetoException {
    User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new org.vcell.util.document.KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    if (lg.isTraceEnabled())
        lg.trace("Testing SimContext with key '" + simContextKey + "'");
    // get biomodel refs
    java.sql.Connection con = null;
    java.sql.Statement stmt = null;
    con = conFactory.getConnection(new Object());
    cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
    cbit.vcell.modeldb.BioModelTable bmTable = cbit.vcell.modeldb.BioModelTable.table;
    cbit.vcell.modeldb.UserTable userTable = cbit.vcell.modeldb.UserTable.table;
    String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + "," + bmTable.ownerRef.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + bmscTable.getTableName() + "," + bmTable.getTableName() + "," + userTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKey + " AND " + bmTable.id.getQualifiedColName() + " = " + bmscTable.bioModelRef.getQualifiedColName() + " AND " + bmTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    ArrayList<KeyValue> bioModelKeys = new ArrayList<KeyValue>();
    stmt = con.createStatement();
    User owner = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
            bioModelKeys.add(key);
            KeyValue ownerRef = new KeyValue(rset.getBigDecimal(bmTable.ownerRef.getUnqualifiedColName()));
            String userid = rset.getString(userTable.userid.getUnqualifiedColName());
            owner = new User(userid, ownerRef);
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
        con.close();
    }
    // use the first biomodel...
    if (bioModelKeys.size() == 0) {
        throw new RuntimeException("zombie simContext ... no biomodels");
    }
    BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(owner, bioModelKeys.get(0));
    // 
    // read in the BioModel from the database
    // 
    BigString bioModelXML = dbServerImpl.getBioModelXML(owner, bioModelInfo.getVersion().getVersionKey());
    BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // ---> only for the SimContext we started with...
    // recompute mathDescription, and verify it is equivalent
    // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
    // 
    SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
    SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
    SimulationContext simContextFromDB = null;
    SimulationContext simContextNewMath = null;
    for (int k = 0; k < simContextsFromDB.length; k++) {
        // find it...
        if (simContextsFromDB[k].getKey().equals(simContextKey)) {
            simContextFromDB = simContextsFromDB[k];
            simContextNewMath = simContextsNewMath[k];
            break;
        }
    }
    if (simContextFromDB == null) {
        throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
    } else {
        MathDescription origMathDesc = simContextFromDB.getMathDescription();
        // 
        try {
            if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        // 
        // updated mathDescription loaded into copy of bioModel, then test for equivalence.
        // 
        cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
        MathDescription mathDesc_latest = mathMapping.getMathDescription();
        MathMapping_4_8 mathMapping_4_8 = new MathMapping_4_8(simContextNewMath);
        MathDescription mathDesc_4_8 = mathMapping_4_8.getMathDescription();
        String issueString = null;
        org.vcell.util.Issue[] issues = mathMapping.getIssues();
        if (issues != null && issues.length > 0) {
            StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):\n");
            for (int l = 0; l < issues.length; l++) {
                buffer.append(" <<" + issues[l].toString() + ">>\n");
            }
            issueString = buffer.toString();
        }
        simContextNewMath.setMathDescription(mathDesc_latest);
        MathCompareResults mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_latest);
        MathCompareResults mathCompareResults_4_8 = null;
        try {
            mathCompareResults_4_8 = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_4_8);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            mathCompareResults_4_8 = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, e.getMessage());
        }
        return new MathGenerationResults(bioModelFromDB, simContextFromDB, origMathDesc, mathDesc_latest, mathCompareResults_latest, mathDesc_4_8, mathCompareResults_4_8);
    }
}

Example 17 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class ModelTable method readRbmElement.

public static void readRbmElement(Connection con, Model model, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    Statement stmt = null;
    try {
        stmt = con.createStatement();
        ResultSet rset = stmt.executeQuery("SELECT * FROM " + ModelTable.table.getTableName() + " WHERE " + ModelTable.table.id.getUnqualifiedColName() + " = " + model.getVersion().getVersionKey().toString());
        if (rset.next()) {
            String rbmXMLStr = DbDriver.varchar2_CLOB_get(rset, ModelTable.table.rbmSmall, ModelTable.table.rbmLarge, dbSyntax);
            rset.close();
            if (rbmXMLStr != null) {
                Element rbmElement = XmlUtil.stringToXML(rbmXMLStr, null).getRootElement();
                XmlReader reader = new XmlReader(false);
                try {
                    reader.getRbmModelContainer(rbmElement, model);
                } catch (ModelException | PropertyVetoException | XmlParseException e) {
                    throw new DataAccessException(e.getMessage(), e);
                }
            }
        }
    } finally {
        if (stmt != null) {
            try {
                stmt.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 18 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class ServerDocumentManager method getBioModelXML.

/**
 * Insert the method's description here.
 * Creation date: (3/29/2004 4:04:16 PM)
 * @return java.lang.String
 * @param vType cbit.sql.VersionableType
 * @param vKey cbit.sql.KeyValue
 */
public String getBioModelXML(QueryHashtable dbc, User user, KeyValue bioModelKey, boolean bRegenerateXML) throws DataAccessException {
    String bioModelXML = null;
    try {
        bioModelXML = dbServer.getDBTopLevel().getBioModelXML(user, bioModelKey, true);
        if (bioModelXML != null) {
            if (bRegenerateXML) {
                try {
                    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML));
                    return cbit.vcell.xml.XmlHelper.bioModelToXML(bioModel);
                } catch (XmlParseException e) {
                    e.printStackTrace();
                    throw new DataAccessException(e.getMessage(), e);
                }
            } else {
                return bioModelXML;
            }
        }
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
    // 
    // not stored as XML currently, retrieve traditional way.
    // 
    }
    try {
        bioModelXML = getBioModelUnresolved(dbc, user, bioModelKey);
        dbServer.insertVersionableXML(user, VersionableType.BioModelMetaData, bioModelKey, bioModelXML);
        return bioModelXML;
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (cbit.vcell.xml.XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
}

Example 19 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class SimContextTable method readAppComponents.

/**
 * readAppComponents : reads the additional simContext components like bioevents/application related flags (for stochastic, at the moment), if present, and sets them on simContext.
 * @param con
 * @param simContext
 * @return
 * @throws SQLException
 * @throws DataAccessException
 * @throws PropertyVetoException
 */
public void readAppComponents(Connection con, SimulationContext simContext, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, PropertyVetoException {
    try {
        Element appComponentsElement = getAppComponentsElement(con, simContext.getVersion().getVersionKey(), dbSyntax);
        if (appComponentsElement != null) {
            Element appRelatedFlags = appComponentsElement.getChild(XMLTags.ApplicationSpecificFlagsTag);
            if (appRelatedFlags != null) {
                // for now, only reading the 'randomizeInitCondition' attribute, since 'isStoch' and 'isUsingconcentration' are read in by other means; so not messing with those fields of simContext.
                boolean bRandomizeInitCondition = false;
                if ((appRelatedFlags.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (appRelatedFlags.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
                    bRandomizeInitCondition = true;
                }
                simContext.setRandomizeInitConditions(bRandomizeInitCondition);
            }
            if ((appComponentsElement.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (appComponentsElement.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))) {
                simContext.setInsufficientIterations(true);
            } else {
                simContext.setInsufficientIterations(false);
            }
            if ((appComponentsElement.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (appComponentsElement.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))) {
                simContext.setInsufficientMaxMolecules(true);
            } else {
                simContext.setInsufficientMaxMolecules(false);
            }
            XmlReader xmlReader = new XmlReader(false);
            NetworkConstraints nc = null;
            Element ncElement = appComponentsElement.getChild(XMLTags.RbmNetworkConstraintsTag);
            if (ncElement != null) {
                // one network constraint element
                nc = xmlReader.getAppNetworkConstraints(ncElement, simContext.getModel());
            }
            simContext.setNetworkConstraints(nc);
            // get spatial objects
            Element spatialObjectsElement = appComponentsElement.getChild(XMLTags.SpatialObjectsTag);
            if (spatialObjectsElement != null) {
                SpatialObject[] spatialObjects = xmlReader.getSpatialObjects(simContext, spatialObjectsElement);
                simContext.setSpatialObjects(spatialObjects);
            }
            // get application parameters
            Element appParamsElement = appComponentsElement.getChild(XMLTags.ApplicationParametersTag);
            if (appParamsElement != null) {
                SimulationContextParameter[] appParams = xmlReader.getSimulationContextParams(appParamsElement, simContext);
                simContext.setSimulationContextParameters(appParams);
            }
            // get bioEvents
            Element bioEventsElement = appComponentsElement.getChild(XMLTags.BioEventsTag);
            if (bioEventsElement != null) {
                BioEvent[] bioEvents = xmlReader.getBioEvents(simContext, bioEventsElement);
                simContext.setBioEvents(bioEvents);
            }
            // get spatial processes
            Element spatialProcessesElement = appComponentsElement.getChild(XMLTags.SpatialProcessesTag);
            if (spatialProcessesElement != null) {
                SpatialProcess[] spatialProcesses = xmlReader.getSpatialProcesses(simContext, spatialProcessesElement);
                simContext.setSpatialProcesses(spatialProcesses);
            }
            // get microscope measurements
            Element element = appComponentsElement.getChild(XMLTags.MicroscopeMeasurement);
            if (element != null) {
                xmlReader.getMicroscopeMeasurement(element, simContext);
            }
            // get rate rules
            Element rateRulesElement = appComponentsElement.getChild(XMLTags.RateRulesTag);
            if (rateRulesElement != null) {
                RateRule[] rateRules = xmlReader.getRateRules(simContext, rateRulesElement);
                simContext.setRateRules(rateRules);
            }
            // get reaction rule specs
            Element reactionRuleSpecsElement = appComponentsElement.getChild(XMLTags.ReactionRuleSpecsTag);
            if (reactionRuleSpecsElement != null) {
                ReactionRuleSpec[] reactionRuleSpecs = xmlReader.getReactionRuleSpecs(simContext, reactionRuleSpecsElement);
                simContext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs);
            }
        }
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("Error retrieving bioevents : " + e.getMessage());
    }
}

Example 20 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class VCDatabaseScanner method scanMathModels.

public void scanMathModels(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleMathmodelKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    BadMathVisitor badMathVisitor = null;
    if (databaseVisitor instanceof BadMathVisitor) {
        badMathVisitor = (BadMathVisitor) databaseVisitor;
    }
    final boolean isBadMathVisitor = badMathVisitor != null;
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning mathmodels ......");
        logFilePrintStream.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            MathModelInfo[] mathInfos = dbServerImpl.getMathModelInfos(user, false);
            for (int j = 0; j < mathInfos.length; j++) {
                if (singleMathmodelKey != null && !mathInfos[j].getVersion().getVersionKey().compareEqual(singleMathmodelKey)) {
                    System.out.println("skipping geometry, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(mathInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping geometry with key '" + mathInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(mathInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including geometry with key '" + mathInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterMathModel(mathInfos[j])) {
                    continue;
                }
                KeyValue vk = null;
                try {
                    vk = mathInfos[j].getVersion().getVersionKey();
                    BigString mathModelXML = dbServerImpl.getMathModelXML(user, mathInfos[j].getVersion().getVersionKey());
                    MathModel mathModel = cbit.vcell.xml.XmlHelper.XMLToMathModel(new XMLSource(mathModelXML.toString()));
                    mathModel.refreshDependencies();
                    databaseVisitor.visitMathModel(mathModel, logFilePrintStream);
                } catch (Exception e2) {
                    if (isBadMathVisitor) {
                        badMathVisitor.unableToLoad(vk, e2);
                    }
                    lg.error(e2.getMessage(), e2);
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        System.err.println("error writing to log file.");
    }
}